V3V4 region silva database

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I am planning to analyze my 16S RNA sequences using Galaxy mothur Toolset.

I watched your youtube Tutorial GTN Training - Microbial Analysis - 16S Metagenomics and analyzed some test samples following the

But the problem is that my PCR amplification targeted the V3V4 region of the 16s rRNA, using the primers set 341F and 806R.

Can I still use the silvav4fasta database for alignment? Does it cover this region?

I tried downloading the latest version of silva 138.1 but there is an error and I cannot perform the align.seqs command.

I tried changing in silvav4 the start and end in the screen.seqs command but it didn’t work as well.

Could anyone please advise regarding this matter?
Thank you!!

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Hi @Funnyme186,

you should generate a customized datase to our region of interest using the pcr.seqs command on the mothur-compatible dataset: Silva reference files.

Where did you get this dataset from?

I recommend you to have a look at the following resources, which could help you to solve some your your doubts:

Regards

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